Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks,Christian Rinke,Maria Chuvochina,Pierre-Alain Chaumeil,Ben J. Woodcroft,Paul N. Evans,Philip Hugenholtz,Gene W. Tyson +7 more
TLDR
The recovery of 7,903 bacterial and archaeal metagenome-assembled genomes increases the phylogenetic diversity represented by public genome repositories and provides the first representatives from 20 candidate phyla.Abstract:
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.read more
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Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit
Fernando Meyer,Till Robin Lesker,David Koslicki,Adrian Fritz,Alexey Gurevich,Aaron E. Darling,Alexander Sczyrba,Andreas Bremges,Alice C. McHardy +8 more
TL;DR: This tutorial describes emerging standards in computational metaomics benchmarking derived and agreed upon by a larger community of researchers and outlines recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative.
Journal ArticleDOI
Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides
Lucélia Cabral,Gabriela F. Persinoti,Douglas A. A. Paixão,Marcele Pandeló Martins,Mariana A. B. Morais,Mariana Chinaglia,Mariane Noronha Domingues,Maurício L. Sforça,Renan A. S. Pirolla,Wesley Cardoso Generoso,Clelton A. Santos,Lucas F. Maciel,Nicolas Terrapon,Vincent Lombard,Bernard Henrissat,Mário T. Murakami +15 more
TL;DR: In this paper , the largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive.
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Defining the Rhizobium Leguminosarum Species Complex
J. Peter W. Young,Sara Moeskjær,Alexey M. Afonin,Praveen Rahi,Marta Maluk,Euan K. James,Maria Izabel A. Cavassim,M. Harun-or Rashid,Aregu Amsalu Aserse,Benjamin J. Perry,En Tao Wang,Encarna Velázquez,Evgeny E. Andronov,Anastasia P. Tampakaki,José David Flores Félix,Raúl Rivas González,Sameh H. Youseif,Marc Lepetit,Stéphane Boivin,Beatriz Jorrin,Gregory Kenicer,Alvaro Peix,Michael F. Hynes,Martha-Helena Ramírez-Bahena,Arvind Gulati,Chang Fu Tian +25 more
TL;DR: It is concluded that access to a large number of genome sequences is a powerful tool for characterising the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
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Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy
Christian Rinke,Maria Chuvochina,Aaron J. Mussig,Pierre-Alain Chaumeil,Adrián A. Davín,David W. Waite,William B. Whitman,Donovan H. Parks,Philip Hugenholtz +8 more
TL;DR: This paper proposed a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence.
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Comprehensive ecosystem-specific 16S rRNA gene databases with automated taxonomy assignment (AutoTax) provide species-level resolution in microbial ecology
Morten Simonsen Dueholm,Kasper Skytte Andersen,Francesca Petriglieri,Simon Jon McIlroy,Marta Nierychlo,Jette Fischer Petersen,Jannie Munk Kristensen,Erika Yashiro,Søren Michael Karst,Mads Albertsen,Per Halkjær Nielsen +10 more
TL;DR: The novel approach allows consistent species-level classification of 16S rRNA amplicons sequence variants and the design of highly specific oligonucleotide probes for fluorescence in situ hybridization, which can reveal in situ properties of microbes at unprecedented taxonomic resolution.
References
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